Rig pose of proxy armature isn't saved

This is due to protected layers on the armature. https://docs.blender.org/manual/en/latest/animation/armatures/properties/skeleton.html#protected-layers

Also, keyframing your poses is always a good idea, and quite the opposite of hacky. If you aren't keyframing your poses you're hanging by a thread, and opening yourself up to various ways of losing said posing, this being only one of them!

I'm using Blender 2.90.0 Alpha (released on 2020-06-22 at 22:06) and the Rain v2.0 model from Blender Cloud (https://cloud.blender.org/p/characters/5f04a68bb5f1a2612f7b29da). I ran into the same issue, the import instructions on other characters say to:

(paraphrased)

1. Center your 3D cursor. File > Link > [character file.blend]
2. Collections > CH-[character], then press Enter.
3. Select the Collection in the Viewport.
4. Object > Relations > Make Proxy...
5. Select RIG-[character].
6. Pose the proxy to your liking.

I've discovered that if you create a new Action in the Action Editor (inside of Dope Sheet) then jump to frame 0 (or 1, whichever suits your workflow better) and keyframe ALL bones (enable all hidden bones beforehand just to make sure all are selected), then turn on Auto Keying, it saves the action with all the keys to make sure your pose is saved when you save the .blend file. Let me know if you need more detailed instructions, I kind of glossed over it because of the limited time I have to write this at the moment. I realize this is a hacky way of saving the pose, but it's the only workaround I know of so far.